Mercurial > repos > bebatut > extract_sequence_file

annotate extract_sequence_file.xml @ 0:14fd6f3b0898 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
author bebatut
date Wed, 27 Jan 2016 02:50:51 -0500
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14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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1 <tool id="extract_sequence_file" name="Extract" version="0.1.0">
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2
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3 <description>from sequence file</description>
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4
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5 <macros>
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6 <xml name="fasta_option">
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7 <option value="id">Identifiant</option>
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8 <option value="length">Length</option>
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9 <option value="description">Description</option>
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10 </xml>
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11 <xml name="fastq_option">
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12 <option value="id">Identifiant</option>
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13 <option value="length">Length</option>
14fd6f3b0898 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/extract_sequence_file/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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14 <option value="description">Description</option>
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15 </xml>
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16 <xml name="test_constrain_extraction">
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17 <param name='constrained_extraction' type='boolean' checked="false"
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18 truevalue='true' falsevalue='false' label="Constrain extraction?" help=""/>
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19 </xml>
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20 <xml name="constrain_string">
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21 <conditional name="constraint_type">
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22 <param name="type" type="select" display="radio" label="Type of
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23 constraint" help="">
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24 <option value="equal">Equal a value</option>
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25 <option value="in">In a list</option>
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26 <option value="not_in">Not in a list</option>
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27 </param>
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28 <when value="equal">
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29 <param name="value" type="text" size="200" label="Equal to"
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30 help=""/>
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31 <validator type="empty_field" message="Give a value"/>
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32 </when>
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33 <when value="in">
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34 <param format="txt" name="value" type="data" label="List of
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35 constraint" help="Text file with a value per line and
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36 nothing else"/>
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37 <validator type="unspecified_build" message="Select a file"/>
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38 </when>
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39 <when value="not_in">
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40 <param format="txt" name="value" type="data" label="List of
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41 constraint" help="Text file with a value per line and
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42 nothing else"/>
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43 <validator type="unspecified_build" message="Select a file"/>
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44 </when>
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45 </conditional>
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46 </xml>
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47 <xml name="constrain_number">
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48 <param name="type" type="select" label="Type of constraint" help="">
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49 <option value="equal">Equal to </option>
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50 <option value="lower">Lower than </option>
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51 <option value="strictly_lower">Strictly lower than </option>
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52 <option value="greater">Greater than </option>
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53 <option value="strictly_greater">Strictly greater than </option>
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54 </param>
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55 </xml>
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56 <xml name="constraint_definitions">
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57 <conditional name="constraints">
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58 <expand macro="test_constrain_extraction" />
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59 <when value="true">
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60 <repeat name="constraint_definition" title="Constraints on
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61 sequences" min="1">
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62 <conditional name="constrained_information">
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63 <param name="info_to_constrain" type="select"
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64 label="Information to constrain" help="">
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65 <option value="id">Identifiant</option>
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66 <option value="length">Length</option>
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67 </param>
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68 <when value="id">
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69 <expand macro="constrain_string" />
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70 </when>
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71 <when value="length">
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72 <repeat name="constraint_definition" title="Constraint
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73 on sequence length" min="1">
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74 <expand macro="constrain_number" />
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75 <param name="value" type="integer" min="0"
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76 max="3000" value="100" label="Value" help=""/>
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77 </repeat>
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78 </when>
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79 </conditional>
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80 </repeat>
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81 </when>
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82 <when value="false" />
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83 </conditional>
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84 </xml>
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85 </macros>
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86
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87 <requirements>
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88 </requirements>
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89
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90 <stdio>
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91 </stdio>
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92
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93 <version_command><![CDATA[python -version]]></version_command>
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94
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95 <!--<command>-->
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96 <command><![CDATA[
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97 python $__tool_directory__/extract_sequence_file.py
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98 --input=$sequence_file_format.sequence_file
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99
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100 --custom_extraction_type=$sequence_file_format.extraction.specific_extraction
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101 #if $sequence_file_format.extraction.specific_extraction :
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102 --to_extract="{$sequence_file_format.extraction.to_extract}"
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103 --output_information=$information_file
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104 #else if $sequence_file_format.format=="fastq":
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105 --split=$sequence_file_format.extraction.split.split_test
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106 #if $sequence_file_format.extraction.split.split_test :
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107 --quality_format=$sequence_file_format.extraction.split.quality_format
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108 --output_sequence=$fasta_sequence_file_from_fastq
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109 --output_quality=$quality_file
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110 #else:
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111 --output_sequence=$fastq_sequence_file
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112 #end if
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113 #else:
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114 --output_sequence=$fasta_sequence_file
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115 #end if
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116
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117 #if $constraints.constrained_extraction :
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118 #for $i, $constrain in enumerate( $constraints.constraint_definition )
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119 #set info_to_constrain=$constrain.constrained_information['info_to_constrain']
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120 #if $info_to_constrain in ("id"):
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121 --constraint="$info_to_constrain:
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122 ${constrain.constrained_information.constraint_type.type}:
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123 ${constrain.constrained_information.constraint_type.value}"
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124 #else:
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125 #for $j, $sub_constrain in enumerate( $constrain.constrained_information.constraint_definition )
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126 --constraint="$info_to_constrain:
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127 ${sub_constrain.type}:
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128 ${sub_constrain.value}"
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129 #end for
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130 #end if
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131 #end for
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132 #end if
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133
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134 --report $report_filepath
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135 --format=$sequence_file_format.format
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136 ]]>
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137 </command>
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138
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139 <inputs>
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140 <conditional name="sequence_file_format">
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141 <param name="format" type="select" display="radio"
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142 label="Format of the sequence file" help="">
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143 <option value="fasta">Fasta</option>
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144 <option value="fastq">FastQ</option>
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145 </param>
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146 <when value="fastq">
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147 <param name="sequence_file" type="data" format="fastq"
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148 label="Sequence file" help=""/>
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149 <conditional name="extraction">
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150 <param name='specific_extraction' type='boolean'
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151 checked="false" truevalue='true' falsevalue='false'
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152 label="Extract specific information?"
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153 help="If no is selected, a sequence file is generated.
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154 If yes, a text file containing the wanted information is
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155 generated"/>
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156 <when value="true">
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157 <param name="to_extract" type="select" display="checkboxes"
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158 multiple="true" label="Information to extract" help="">
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159 <expand macro="fasta_option" />
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160 <validator type="no_options" message="Select at least
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161 one information to extract"/>
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162 </param>
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163 </when>
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164 <when value="false">
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165 <conditional name="split">
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166 <param name='split_test' type='boolean' checked="false"
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167 truevalue='true' falsevalue='false' label="Split
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168 file into sequence and quality files?" help="If
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169 yes is selected, a fasta and a quality file are
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170 generated. If no, a fastq file is generated"/>
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171 <when value="true">
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172 <param name="quality_format" type="select"
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173 display="radio" label="Coding of quality
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174 scores?" help="">
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175 <option value="sanger" selected="true">Sanger (Phred+33)</option>
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176 <option value="solexa">Solexa (Solexa+64) </option>
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177 <option value="illumina_1_3">Illumina 1.3+ (Phred+64) </option>
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178 <option value="illumina_1_5">Illumina 1.5+ (Phred+64) </option>
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179 <option value="illumina_1_8">Illumina 1.8+ (Phred+33) </option>
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180 </param>
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181 </when>
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182 <when value="false" />
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183 </conditional>
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184 </when>
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185 </conditional>
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186 </when>
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187 <when value="fasta">
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188 <param name="sequence_file" type="data" format="fasta"
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189 label="Sequence file" help=""/>
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190 <conditional name="extraction">
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191 <param name='specific_extraction' type='boolean' checked="false"
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192 truevalue='true' falsevalue='false' label="Extract specific
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193 information?" help="If no is selected, a sequence file is
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194 generated. If yes, a text file containing the wanted
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195 information is generated"/>
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196 <when value="true">
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197 <param name="to_extract" type="select" display="checkboxes"
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198 multiple="true" label="Information to extract" help="">
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199 <expand macro="fasta_option" />
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200 <validator type="no_options" message="Select at least
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201 one information to extract"/>
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202 </param>
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203 </when>
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204 <when value="false" />
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205 </conditional>
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206 </when>
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207 </conditional>
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208
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209 <expand macro="constraint_definitions" />
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210 </inputs>
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211
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212 <outputs>
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213 <data format="txt" name="information_file"
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214 label="${tool.name} on ${on_string}: Information">
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215 <filter>((sequence_file_format['extraction']['specific_extraction']))</filter>
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216 </data>
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217
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218 <data format="fasta" name="fasta_sequence_file"
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219 label="${tool.name} on ${on_string}: Extracted sequences" >
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220 <filter>((sequence_file_format['format'] == 'fasta' and
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221 not sequence_file_format['extraction']['specific_extraction']))</filter>
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222 </data>
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223
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224 <data format="fastq" name="fastq_sequence_file"
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225 label="${tool.name} on ${on_string}: Extracted sequences">
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226 <filter>((sequence_file_format['format'] == 'fastq' and
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227 not sequence_file_format['extraction']['specific_extraction'] and
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228 not sequence_file_format['extraction']['split']['split_test']))</filter>
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229 </data>
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230
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231 <data format="qual" name="quality_file"
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232 label="${tool.name} on ${on_string}: Extracted quality">
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233 <filter>((sequence_file_format['format'] == 'fastq' and
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234 not sequence_file_format['extraction']['specific_extraction'] and
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235 sequence_file_format['extraction']['split']['split_test']))</filter>
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236 </data>
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237
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238 <data format="fasta" name="fasta_sequence_file_from_fastq"
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239 label="${tool.name} on ${on_string}: Extracted sequences">
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240 <filter>((sequence_file_format['format'] == 'fastq' and
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241 not sequence_file_format['extraction']['specific_extraction'] and
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242 sequence_file_format['extraction']['split']['split_test']))</filter>
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243 </data>
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244
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245 <data format="txt" name="report_filepath"
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246 label="${tool.name} on ${on_string}: Report"/>
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247 </outputs>
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248
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249 <tests>
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250 <test>
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251 <param name="sequence_file_format.sequence_file"
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252 value="read_write_fasta_file/input_sequence_file.fasta"/>
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253 <param name="sequence_file_format.extraction.specific_extraction"
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254 value="false"/>
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255 <param name="$sequence_file_format.format" value="fasta" />
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256 <output name="fasta_sequence_file"
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257 file="read_write_fasta_file/input_sequence_file.fasta"/>
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258 <output name="report_filepath"
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259 file="read_write_fasta_file/expected_output_report.txt"/>
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260 </test>
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261 </tests>
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262
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263 <help><![CDATA[
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264
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265 **What it does**
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266
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267 This tool extracts information from sequence files.
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268
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269 Some constraints could be added to extraction. For example, you choose
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270 to extract only sequences for which the length is greater than 30 bp.
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271
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272 More information on `ASaiM documentation <http://asaim.readthedocs.org/>`_...
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273
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274 -----
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275
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276 **Input**
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277
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278 The input is one file in fasta or fastq.
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279
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280 -----
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281
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282 **Outputs**
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283
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284 The tool generates different outputs given the choosen parameters:
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285
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286 - a sequence file
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287 - a text file
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288 - a sequence file and a quality file
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289
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290 ]]>
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291 </help>
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292
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293 <citations>
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294 </citations>
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295 </tool>
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296